mri_surfcluster only works for surfaces (that's what the "surf" in the name means). If you want the centroid of a volume ROI use https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids
On 05/02/2018 12:08 PM, Lucia Billeci wrote: > > > Dear Bruce, > > the ROI appears correct in freeview. However I have a problem in the > following step, i.e. obtain the centroid of the ROi. > > I used the following command: > > mri_surfcluster --in > /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel > ./tests_label/sub/lh.amygdala.label --sum > ./tests_label/sum/sum.lh.amygdala --centroid --thmin 0 --hemi lh > --subject fsaverage —nofixmni > > However it doesn’t work for subcortical label files (it works with > cortical ones). I have the following output and the command doesn’t > produce the file sum.lh.amygdala: > > thsign = abs, id = 0 > version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman > Exp $ > hemi = lh > srcid = > /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness > srcsubjid = fsaverage > srcsurf = white > srcframe = 0 > thsign = abs > thmin = 0 > thmax = -1 > fdr = -1 > minarea = 0 > xfmfile = talairach.xfm > clabelfile = ./tests_label/sub/lh.amygdala.label > clabelinv = 0 > nth = -1 > sumfile = ./tests_label/sum/sum.lh.amygdala > subjectsdir = /Applications/freesurfer/subjects > FixMNI = 0 > Loading clabel ./tests_label/sub/lh.amygdala.label. > Found 1941 points in clabel. > ------------- XFM matrix (RAS2RAS) --------------- > /Applications/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm > 1.00000 0.00000 0.00000 0.00000; > 0.00000 1.00000 0.00000 0.00000; > 0.00000 0.00000 1.00000 0.00000; > 0.00000 0.00000 0.00000 1.00000; > ---------------------------------------------------- > Reading source surface > /Applications/freesurfer/subjects/fsaverage/surf/lh.white > Done reading source surface > Computing metric properties > Loading source values > /Applications/freesurfer/bin/mri_surfcluster: line 3: 2828 Bus error: > 10 mri_surfcluster.bin "$@" > > Maybe because lh.thickness is only for cortical regions? In this case, > how can I obtain centroids of subcortical ROIs? > > Thanks > Regards > Lucia > > > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > Dr. Lucia Billeci, PhD > Institute of Clinical Physiology (IFC) National Research Council (CNR) > via Moruzzi 1, 56124, Pisa, Italy > e-mail: lucia.bill...@ifc.cnr.it <mailto:lucia.bill...@ifc.cnr.it> > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > > > >> On 2 May 2018, at 17:05, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >> >> Hi Lucia >> >> the first column being -1 means that it is not mapped to the surface, >> so is correct in your (subcortical) case. Try loading the label as an >> ROI in freeview and see if it is correct >> >> cheers >> Bruce >> On Wed, 2 May 2018, Lucia Billeci wrote: >> >>> External Email - Use Caution >>> Dear Brouce, >>> thanks again. >>> I would like exactly how to set mri_vol2label for subcortical >>> regions as the way I used >>> give me all the values of the first column equal to -1. This is a >>> problem when I want >>> to obtain obtain the centroid of the ROI using mri_surfcluster as I >>> get an empty file. >>> Hope Doug can help me. >>> Thanks >>> Lucia >>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>> Dr. Lucia Billeci, PhD >>> Institute of Clinical Physiology (IFC) National Research Council (CNR) >>> via Moruzzi 1, 56124, Pisa, Italy >>> e-mail: lucia.bill...@ifc.cnr.it <mailto:lucia.bill...@ifc.cnr.it> >>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>> >>> On 2 May 2018, at 16:01, Bruce Fischl >>> <fis...@nmr.mgh.harvard.edu> wrote: >>> Hi Lucia >>> can you cc the list so others can answer? You can't get a >>> surface-based label for >>> a subcortical region as they aren't on (or close) to the surrface. I >>> think >>> mri_vol2label is the right binary to create a volumetric ROI for >>> each one, but >>> Doug will know >>> cheers >>> Bruce >>> On Wed, 2 May 2018, Lucia Billeci wrote: >>> >>> External Email - Use Caution >>> Dear Bruce, >>> thanks for your answer. >>> I would like to obtain .label file for each subcortical region. I >>> have tried the commands I >>> reported in the previous messages but probably they are not >>> correct. >>> Could you please indicate me >>> the correct way to have the .label file for subcortical >>> regions? I am >>> not sure if >>> using mri_vol2label is the right way or maybe there is another >>> strategy. >>> Thanks >>> regards >>> Lucia >>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>> Dr. Lucia Billeci, PhD >>> Institute of Clinical Physiology (IFC) National Research Council >>> (CNR) >>> via Moruzzi 1, 56124, Pisa, Italy >>> e-mail: lucia.bill...@ifc.cnr.it >>> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >>> The information in this e-mail is intended only for the person to >>> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >>> the e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you in error >>> but does not contain patient information, please contact the sender >>> and properly >>> dispose of the e-mail. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
